The RNA-binding protein SUP-12 controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans

Tissue-specific alternative pre-mRNA splicing is essential for increasing diversity of functionally different gene products. In Caenorhabditis elegans, UNC-60A and UNC-60B, nonmuscle and muscle isoforms of actin depolymerizing factor (ADF)/cofilin, are expressed by alternative splicing of unc-60 and regulate distinct actin-dependent developmental processes. We report that SUP-12, a member of a new family of RNA recognition motif (RRM) proteins, including SEB-4, regulates muscle-specific splicing of unc-60. In sup-12 mutants, expression of UNC-60B is decreased, whereas UNC-60A is up-regulated in muscle. sup-12 mutations strongly suppress muscle defects in unc-60B mutants by allowing expression of UNC-60A in muscle that can substitute for UNC-60B, thus unmasking their functional redundancy. SUP-12 is expressed in muscle and localized to the nuclei in a speckled pattern. The RRM domain of SUP-12 binds to several sites of the unc-60 pre-mRNA including the UG repeats near the 3'-splice site in the first intron. Our results suggest that SUP-12 is a novel tissue-specific splicing factor and regulates functional redundancy among ADF/cofilin isoforms.     

Changes in pigmentation, bio-optical characteristics and photophysiology, during phytoflagellate succession in mesocosms

Pigmentation, bio-optical characteristics and photophysiology,were studied in mesocosms with different N:P ratios. No significantdifference in biomass or species composition was seen underdifferent nitrogen to phosphorus ratios (N:P), but a temporalsuccession of different flagellate groups was observed in allmesocosms. An initial bloom of prymnesiophytes containing chlorophyll(Chl) c and 19' hexanoyloxyfucoxanthin (19' HOF) was followedby prasinophytes containing Chl b. Electron microscope analysisconfirmed the presence of genera such as Chrysochromulina (Prymnesiophyceae),Tetraselmis and Pyramimonas (Prasinophyceae). Traces of prasinoxanthinin the pigment samples showed that smaller prasinophytes werealso present. Chl b influenced the photophysiology of the prasinophytesresulting in higher Chl a-specific absorption, but a greaterdifference between absorption and scaled fluorescence excitationspectra indicated that light absorbed by Chl b is associatedwith photosystem I (PSI). Since a larger fraction of the lightwas absorbed by chlorophyll in PSI and/or photoprotective carotenoids,the light-saturated Chl a-specific rate of photosynthesis (P^B_m)and maximum light utilization coefficient (^B) decreased when[Chl b] increased. The highest P^B_m values were seen when theratios of fucoxanthins to Chl a were high, indicating that prymnesiophytesmight be more efficient in light harvesting and electron transportthrough photosystem II (PSII) by fucoxanthins and Chl c. Ourresults therefore indicate different light acclimation strategiesin prasinophytes versus prymnesiophytes, which may be reflectedin the successional appearance of these communities in the naturalenvironment. We also suggest that grazing by ciliates and rotiferscaused periodic decreases in phytoplankton biomass, which inturn gave rise to the phytoflagellate succession observed inthe mesocosms.     

Effects of Rhizoctonia infection and drought on peroxidase and chitinase activity in Norway spruce (Picea abies)

Seedlings of Norway spruce were exposed to fungal infection and drought in order to investigate differences in their stress responses on the enzymatic level. Six-week-old seedlings were infected with the root rot fungus Rhizoctonia , or subjected to drought, respectively. Changes at the enzymatic level were more rapid and significantly higher in infected plants in comparison with drought-stressed spruce plants. Rhizoctonia infection resulted in early local and systemic increase in peroxidase and chitinase activity. The most prominent isoforms responding were highly basic peroxidases and chitinases (pI 9–9.5) and several acidic chitinases (pI3–4). An increased intensity of similar peroxidase isoforms was found in drought-affected plants. Two peroxidase isoforms (with pI < 9) accumulated exclusively in response to drought. These results suggest that at an early stage of infection and drought stress, the two stresses can be distinguished by the temporal appearance and isoform profile of peroxidases and chitinases. Changes in enzyme activity appeared before changes in physiological parameters, thus these isoform profiles could be used as early markers of stress conditions in spruce.     

Impaired circulating myeloid DCs from myeloma patients

BACKGROUND: In clinical trials, cancer patients have received immunotherapy based on DCs generated from leukapheresed blood. It would therefore be an advantage to be able to measure blood levels and estimate the phenotype of DC before leukapheresis, to estimate the yield required for preparation of vaccines, or ex vivo stimulation of T cells for adoptive immunotherapy. METHODS: Recently, circulating lineage negative (Lin-) myeloid DC cells and their precursors have been identified by flow cytometry. We apply this strategy to the screening of blood samples from patients with multiple myeloma, in an attempt to characterize and quantitate the subset. By a direct flow cytometry approach, the blood levels of circulating lineage (CD3, CD19, CD14) negative, CD33++, HLA-DR+ cells were estimated before and following ex vivo cell differentiation, and phenotyped by MAbs with specificity against HLA-DR, HLA-ABC, CD1a, CD11c, CD33, CD40, CD49d, CD49e, CD54, CD80, CD83, and CD86. RESULTS: This study demonstrated that multiple myeloma patients have a 50% reduced blood level of Lin-, CD33++, HLA-DR+ myeloid DC, but a DC-precursor level within normal range. Furthermore, GM-CSF and IL-4 ex vivo stimulated DCs demonstrated an impaired up-regulation of the co-stimulatory molecule CD80 and the adhesion molecule CD54. DISCUSSION: These results may have clinical implications as a predictor for yield and functionality of the harvested DCs to be used in vaccination of myeloma patients.     

CO<Subscript>2</Subscript> enrichment,nitrogen fertilization and development of freezing tolerance in Norway spruce

Plant growth and adaptation to cold and freezing temperatures in a CO₂-enriched atmosphere have received little attention despite the predicted effects of elevated CO₂ on plant distribution and productivity. Norway spruce [Picea abies (L.) Karst.] seedlings from latitudinally distinct seed sources (66°N and 60°N) were grown for one simulated growth season under controlled conditions in an atmosphere enriched in CO₂ (70 Pa) and at ambient CO₂ (40 Pa), combined factorially with low (3.6 mM) or high (15.7 mM) concentrations of nitrogen fertilization. There was a clear difference between the two provenances in height growth, in the timing of bud set, and in freezing tolerance. Nitrogen fertilization increased height growth in both provenances, while CO₂ enrichment stimulated height growth only in the southern provenance. We found no significant effects of elevated CO₂ or nitrogen fertilization on the timing of bud set. During cold acclimation, freezing tolerance increased from –10°C to –35°C, and there was a marked increase in all soluble sugars except inositol. Elevated CO₂ in combination with high nitrogen led to a slight increased freezing tolerance in both provenances during the early stages of cold acclimation. However, towards the end of cold acclimation, elevated CO₂ and high nitrogen led to reduced freezing tolerance in the southern provenance, while elevated CO₂ and low nitrogen reduced freezing tolerance in the northern provenance. These results suggest that CO₂ enrichment influences the development of freezing tolerance, and that these responses differ with available nitrogen and between provenances.     

Kinetic and structural characterization of a two-domain streptokinase: dissection of domain functionality

The mammalian protease plasminogen can be activated by bacterial activators, the three-domain (alpha, beta, gamma) streptokinases and the one-domain (alpha) staphylokinases. These activators act as plasmin(ogen) cofactors, and the resulting complexes initiate proteolytic activity of host plasminogen which facilitates bacterial colonization of the host organism. We have investigated the kinetic mechanism of the plasminogen activation mediated by a novel two-domain (alpha, beta) streptokinase isolated from Streptococcus uberis (Sk(U)) with specificity toward bovine plasminogen. The interaction between Sk(U) and plasminogen occurred in two steps: (1) rapid association of the proteins and (2) slow transition to the active complex Sk(U)-PgA. The complex Sk(U)-PgA converted plasminogen to plasmin with the following parameters: K(m) < or = 1.5 microM and k(cat) = 0.55 s(-)(1). The ability of proteolytic fragments of Sk(U) to activate plasminogen was investigated. Only two C-terminal segments (97-261 and 123-261), which both contain the beta-domain (126-261), were shown to be active. They initiated plasminogen activation in complex with plasmin, but not with plasminogen, and thereby exhibited functional similarity to the staphylokinase. The fusion protein His(6)-Sk(U) (i.e., Sk(U) with a small N-terminal tag) acted exclusively in complex with plasmin as well. These observations demonstrate that (1) the N-terminal alpha-domain, including a native N-terminus, was necessary for "virgin" activation of the associated plasminogen in the Sk(U)-PgA complex and (2) the C-terminal beta-domain of Sk(U) is important for recognition of the substrate in the Sk(U)-PgA complex.     

Phylogenetic relationships within the tropical soft coral genera Sarcophyton and Lobophytum (Anthozoa, Octocorallia)

Abstract. The alcyonacean soft coral genera Sarcophyton and Lobophytum are conspicuous, ecologically important members of shallow reef communities throughout the Indo-West Pacific. Study of their ecology is, however, hindered by incomplete knowledge of their taxonomy: most species cannot be identified in the field and the two genera cannot always be distinguished reliably. We used a 735-bp fragment of the octocoral-specific mitochondrial protein-coding gene msh1 to construct a phylogeny for 92 specimens identified to 19 species of Lobophytum and 16 species of Sarcophyton . All phylogenetic methods used recovered a tree with three strongly supported clades. One clade included only morphologically typical Sarcophyton species with a stalk distinct from the polypary, poorly formed club-shaped sclerites in the colony surface, and large spindles in the interior of the stalk. A second clade included only morphologically typical Lobophytum colonies with lobes and ridges on the colony surface, poorly formed clubs in the colony surface, and interior sclerites consisting of oval forms with regular girdles of ornamental warts. The third distinct clade included a mix of Sarcophyton and Lobophytum nominal species with intermediate morphologies. Most of the species in this mixed clade had a polypary that was not distinct from the stalk, and the sclerites in the colony surface were clubs with well-defined heads. Within the Sarcophyton clade, specimens identified as Sarcophyton glaucum belonged to six very distinct genetic sub-clades, suggesting that this morphologically heterogeneous species is actually a cryptic species complex. Our results highlight the need for a complete taxonomic revision of these genera, using molecular data to help confirm species boundaries as well as to guide higher taxonomic decisions.     

Signatures of diversifying selection and convergence acting on passerine Toll‐like receptor 4 in an evolutionary context

Positive selection acting on Toll‐like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host–pathogen molecular co‐adaptation. Much of this research, however, has focused mainly on the identification of sites predicted to be under positive selection, bringing little insight into the functional differences and similarities among species and a limited understanding of convergent evolution in the innate immune molecules. In this study, we provide evidence of phenotypic variability in the avian TLR4 ligand‐binding region (LBR), the direct interface between host and pathogen molecular structures. We show that 55 passerine species vary substantially in the distribution of electrostatic potential on the surface of the receptor, and based on these distinct patterns, we identified four species clusters. Seven of the 34 evolutionarily nonconservative and positively selected residues correspond topologically to sites previously identified as being important for lipopolysaccharide, lipid IVa or MD‐2 binding. Five of these positions codetermine the identity of the charge clusters. Groups of species that host‐related communities of pathogens were predicted to cluster based on their TLR4 LBR charge. Despite some evidence for convergence among taxa, there were no clear associations between the TLR4 LBR charge distribution and any of the general ecological characteristics compared (migration, latitudinal distribution and diet). Closely related species, however, mostly belonged to the same surface charge cluster indicating that phylogenetic constraints are key determinants shaping TLR4 adaptive evolution. Our results suggest that host innate immune evolution is consistent with Fahrenholz's rule on the cospeciation of hosts and their parasites.     

Carboxamide SIRT1 inhibitors block DBC1 binding via an acetylation-independent mechanism

SIRT1 is an NAD⁺-dependent deacetylase that counteracts multiple disease states associated with aging and may underlie some of the health benefits of calorie restriction. Understanding how SIRT1 is regulated in vivo could therefore lead to new strategies to treat age-related diseases. SIRT1 forms a stable complex with DBC1, an endogenous inhibitor. Little is known regarding the biochemical nature of SIRT1-DBC1 complex formation, how it is regulated and whether or not it is possible to block this interaction pharmacologically. In this study, we show that critical residues within the catalytic core of SIRT1 mediate binding to DBC1 via its N-terminal region, and that several carboxamide SIRT1 inhibitors, including EX-527, can completely block this interaction. We identify two acetylation sites on DBC1 that regulate its ability to bind SIRT1 and suppress its activity. Furthermore, we show that DBC1 itself is a substrate for SIRT1. Surprisingly, the effect of EX-527 on SIRT1-DBC1 binding is independent of DBC1 acetylation. Together, these data show that protein acetylation serves as an endogenous regulatory mechanism for SIRT1-DBC1 binding and illuminate a new path to developing small-molecule modulators of SIRT1.